Chlamydia trachomatis(CT) is the leading cause of sexually transmitted diseases (STD) in the developed world. CT infections and their sequelae of pelvic inflammatory disease, ectopic pregnancy, and infertility are responsible for approximately 80% of the estimated $2.5 billion annual cost of these infections in the United States. Further, up to 50% of women become reinfected and are at increased risk for these sequelae. Many reinfections reflect persistence that likely plays an important role in pathogenesis. The major outer membrane protein is considered to be the immunodominant protein of CT. However, the discovery of open reading frames predicted to encode a nine-member polymorphic membrane protein (Prop) gene (pmp) family in the recently published genome sequence of CT serovar D suggest that these Props may also be important in chlamydial biology. Further, CT contains a partial tryptophan biosynthesis operon (trpR, trpA, trpB) not found in a CT mouse strain (MoPn) or other species of Chlamydia. Tryptophan is essential for chlamydial replication, and tryptophan depletion in vitro results in chlamydial persistence. Our hypothesis is that the prop and tryptophan genes may undergo selection that results in differential expression or activity of these proteins that: 1) consequently determine active or persistent infection; and 2) are significantly involved in pathogenesis as an outcome of persistence or outcome of other factors. By analyzing the genetic profile of prototype and serial recurrent and persistent CT STD patient strains and by correlating these data with epidemiologic and clinical findings, we hope to identify the genes, genetic/protein variation and evolution of this variation in the organism, and how these are linked to persistence and pathogenesis. Thus, this grant will answer broad questions about the genetic and protein basis for persistence and for pathogenesis, and provide important research tools including a Database and DNA microarray that will be of long-term benefit to investigators in the field of Chlamydia. The Specific Aims for this grant are to: 1) Sequence the nine pmps, and trpR, trpA, and trpB genes for the 19 prototype serovars of CT and create a DNA microarray for these genes and ompA to differentiate strains of CT, and for use in Aim 2; and 2) Identify polymorphisms in and protein expression of the nine props, specific tryptophan operon genes, and other constitutively expressed genes among serial cervical samples from patients with persistent versus non-persistent CT STDs; correlate the genetic and protein expression profiles of these serial samples with epidemiologic and clinical findings.